Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 85KVY

Calculation Name: 3H3B-C-Xray372

Preferred Name: Receptor protein-tyrosine kinase erbB-2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3H3B

Chain ID: C

ChEMBL ID: CHEMBL1824

UniProt ID: P04626

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2873806.065575
FMO2-HF: Nuclear repulsion 2783065.531714
FMO2-HF: Total energy -90740.533861
FMO2-MP2: Total energy -91004.957644


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(C:-2:GLN)


Summations of interaction energy for fragment #1(C:-2:GLN)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-2.0180.855-0.026-1.392-1.454-0.002
Interaction energy analysis for fragmet #1(C:-2:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.033
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3C0ALA0-0.0210.0003.533-1.6271.208-0.025-1.390-1.420-0.002
4C1ASP-1-0.841-0.9275.3820.2960.334-0.001-0.002-0.0340.000
5C2ILE0-0.042-0.0119.195-0.018-0.0180.0000.0000.0000.000
6C3VAL0-0.011-0.01010.875-0.021-0.0210.0000.0000.0000.000
7C4LEU0-0.001-0.01113.7740.0320.0320.0000.0000.0000.000
8C5THR0-0.011-0.01716.732-0.034-0.0340.0000.0000.0000.000
9C6GLN00.035-0.00719.2910.0160.0160.0000.0000.0000.000
10C7THR0-0.0540.01322.802-0.015-0.0150.0000.0000.0000.000
11C8PRO00.0680.03525.6850.0080.0080.0000.0000.0000.000
12C9SER00.0270.00527.3800.0030.0030.0000.0000.0000.000
13C10SER0-0.018-0.00928.4820.0010.0010.0000.0000.0000.000
14C11LEU0-0.007-0.01931.6280.0000.0000.0000.0000.0000.000
15C12PRO00.0230.02234.2360.0010.0010.0000.0000.0000.000
16C13VAL0-0.009-0.01036.8300.0020.0020.0000.0000.0000.000
17C14SER00.0150.00939.638-0.004-0.0040.0000.0000.0000.000
18C15VAL0-0.028-0.03942.0380.0030.0030.0000.0000.0000.000
19C16GLY0-0.026-0.01542.862-0.002-0.0020.0000.0000.0000.000
20C17GLU-1-0.869-0.92639.7530.0590.0590.0000.0000.0000.000
21C18LYS10.9540.98535.145-0.087-0.0870.0000.0000.0000.000
22C19VAL00.0020.00733.103-0.001-0.0010.0000.0000.0000.000
23C20THR0-0.004-0.01628.7990.0030.0030.0000.0000.0000.000
24C21MET0-0.0230.00927.399-0.004-0.0040.0000.0000.0000.000
25C22THR0-0.003-0.01622.4110.0100.0100.0000.0000.0000.000
26C23CYS0-0.076-0.01819.827-0.004-0.0040.0000.0000.0000.000
27C24LYS10.9680.99017.733-0.190-0.1900.0000.0000.0000.000
28C25SER0-0.033-0.04512.586-0.041-0.0410.0000.0000.0000.000
29C26SER00.0160.01710.1650.0350.0350.0000.0000.0000.000
30C27GLN00.0180.0136.0420.2530.2530.0000.0000.0000.000
31C28THR00.0050.0309.632-0.227-0.2270.0000.0000.0000.000
32C29LEU0-0.009-0.01011.0410.0200.0200.0000.0000.0000.000
33C30LEU0-0.045-0.00413.736-0.059-0.0590.0000.0000.0000.000
34C31TYR00.0030.00612.0810.0960.0960.0000.0000.0000.000
35C32SER00.022-0.01013.622-0.052-0.0520.0000.0000.0000.000
36C33ASN0-0.0030.01015.571-0.042-0.0420.0000.0000.0000.000
37C34ASN00.008-0.01317.550-0.015-0.0150.0000.0000.0000.000
38C35GLN00.0020.00318.3200.0050.0050.0000.0000.0000.000
39C36LYS10.9110.98118.783-0.241-0.2410.0000.0000.0000.000
40C37ASN00.0370.00717.4430.0800.0800.0000.0000.0000.000
41C38TYR0-0.022-0.00115.605-0.036-0.0360.0000.0000.0000.000
42C39LEU0-0.006-0.00117.1430.0010.0010.0000.0000.0000.000
43C40ALA0-0.008-0.00919.395-0.012-0.0120.0000.0000.0000.000
44C41TRP00.011-0.00422.559-0.003-0.0030.0000.0000.0000.000
45C42TYR0-0.042-0.05823.040-0.003-0.0030.0000.0000.0000.000
46C43GLN00.0040.00427.560-0.002-0.0020.0000.0000.0000.000
47C44GLN0-0.002-0.00830.7130.0030.0030.0000.0000.0000.000
48C45LYS10.9500.98332.539-0.078-0.0780.0000.0000.0000.000
49C46PRO00.023-0.00336.1930.0010.0010.0000.0000.0000.000
50C47GLY00.0130.00937.506-0.002-0.0020.0000.0000.0000.000
51C48GLN0-0.041-0.00836.8310.0010.0010.0000.0000.0000.000
52C49SER00.0080.01532.9890.0010.0010.0000.0000.0000.000
53C50PRO0-0.026-0.02328.956-0.002-0.0020.0000.0000.0000.000
54C51LYS10.9480.98031.251-0.089-0.0890.0000.0000.0000.000
55C52LEU0-0.0050.01126.3520.0000.0000.0000.0000.0000.000
56C53LEU0-0.045-0.00928.762-0.006-0.0060.0000.0000.0000.000
57C54ILE0-0.002-0.00525.750-0.004-0.0040.0000.0000.0000.000
58C55SER00.0270.02524.1420.0040.0040.0000.0000.0000.000
59C56TRP0-0.030-0.02719.3320.0020.0020.0000.0000.0000.000
60C57ALA00.0230.03321.2730.0050.0050.0000.0000.0000.000
61C58PHE0-0.042-0.05323.012-0.013-0.0130.0000.0000.0000.000
62C59THR0-0.0140.00926.483-0.013-0.0130.0000.0000.0000.000
63C60ARG10.9020.96928.318-0.110-0.1100.0000.0000.0000.000
64C61LYS10.9440.98130.828-0.110-0.1100.0000.0000.0000.000
65C62SER00.016-0.01032.057-0.005-0.0050.0000.0000.0000.000
66C63GLY00.0190.00835.641-0.001-0.0010.0000.0000.0000.000
67C64VAL0-0.051-0.01032.892-0.004-0.0040.0000.0000.0000.000
68C65PRO00.013-0.00136.0080.0010.0010.0000.0000.0000.000
69C66ASP-1-0.921-0.96735.9710.0900.0900.0000.0000.0000.000
70C67ARG10.7780.85936.535-0.077-0.0770.0000.0000.0000.000
71C68PHE0-0.024-0.00132.1900.0010.0010.0000.0000.0000.000
72C69THR00.007-0.01630.4380.0020.0020.0000.0000.0000.000
73C70GLY00.0120.02026.990-0.001-0.0010.0000.0000.0000.000
74C71SER00.0280.00225.988-0.005-0.0050.0000.0000.0000.000
75C72GLY00.0140.00722.5170.0010.0010.0000.0000.0000.000
76C73SER0-0.024-0.02819.5730.0100.0100.0000.0000.0000.000
77C74GLY00.0630.04315.4340.0000.0000.0000.0000.0000.000
78C75THR00.0300.01612.8320.0390.0390.0000.0000.0000.000
79C76ASP-1-0.905-0.94515.5370.2460.2460.0000.0000.0000.000
80C77PHE00.006-0.00516.591-0.005-0.0050.0000.0000.0000.000
81C78THR0-0.011-0.00621.690-0.012-0.0120.0000.0000.0000.000
82C79LEU0-0.039-0.00625.3050.0040.0040.0000.0000.0000.000
83C80THR0-0.013-0.01728.035-0.009-0.0090.0000.0000.0000.000
84C81ILE0-0.0060.00631.5900.0010.0010.0000.0000.0000.000
85C82GLY0-0.026-0.01734.876-0.004-0.0040.0000.0000.0000.000
86C83SER0-0.014-0.01037.675-0.004-0.0040.0000.0000.0000.000
87C84VAL0-0.0280.00337.0710.0010.0010.0000.0000.0000.000
88C85LYS10.9880.97939.743-0.070-0.0700.0000.0000.0000.000
89C86ALA00.0510.01440.8350.0010.0010.0000.0000.0000.000
90C87GLU-1-0.910-0.95840.3860.0700.0700.0000.0000.0000.000
91C88ASP-1-0.726-0.82436.6690.0820.0820.0000.0000.0000.000
92C89LEU00.0050.05736.1700.0040.0040.0000.0000.0000.000
93C90ALA0-0.009-0.01034.040-0.001-0.0010.0000.0000.0000.000
94C91VAL0-0.0230.00228.839-0.001-0.0010.0000.0000.0000.000
95C92TYR0-0.013-0.04828.4490.0040.0040.0000.0000.0000.000
96C93TYR0-0.009-0.00124.093-0.002-0.0020.0000.0000.0000.000
97C95GLN00.012-0.01018.795-0.005-0.0050.0000.0000.0000.000
98C96GLN00.0770.04612.8900.0380.0380.0000.0000.0000.000
99C97TYR0-0.017-0.01916.281-0.013-0.0130.0000.0000.0000.000
100C98SER0-0.018-0.00811.672-0.004-0.0040.0000.0000.0000.000
101C99ASN00.0120.0008.331-0.059-0.0590.0000.0000.0000.000
102C100TYR0-0.057-0.00510.496-0.020-0.0200.0000.0000.0000.000
103C101PRO00.0310.0059.7730.0110.0110.0000.0000.0000.000
104C102TRP00.0390.00113.302-0.019-0.0190.0000.0000.0000.000
105C103THR0-0.040-0.03114.260-0.010-0.0100.0000.0000.0000.000
106C104PHE00.000-0.01316.8760.0070.0070.0000.0000.0000.000
107C105GLY00.0460.03419.1460.0000.0000.0000.0000.0000.000
108C106GLY0-0.039-0.04120.702-0.008-0.0080.0000.0000.0000.000
109C107GLY0-0.036-0.01923.326-0.009-0.0090.0000.0000.0000.000
110C108THR0-0.033-0.02925.968-0.001-0.0010.0000.0000.0000.000
111C109ARG10.9190.94928.719-0.061-0.0610.0000.0000.0000.000
112C110LEU00.0030.01532.195-0.002-0.0020.0000.0000.0000.000
113C111GLU-1-0.949-0.97634.9120.0550.0550.0000.0000.0000.000
114C112ILE00.0340.02638.368-0.001-0.0010.0000.0000.0000.000
115C135GLU-1-0.860-0.94739.2730.0790.0790.0000.0000.0000.000
116C136VAL0-0.104-0.03133.3390.0010.0010.0000.0000.0000.000
117C137GLN0-0.030-0.01736.792-0.002-0.0020.0000.0000.0000.000
118C138LEU0-0.005-0.02531.0170.0020.0020.0000.0000.0000.000
119C139GLN0-0.0180.00135.327-0.003-0.0030.0000.0000.0000.000
120C140GLN0-0.001-0.02932.3270.0040.0040.0000.0000.0000.000
121C141SER00.0500.03236.422-0.002-0.0020.0000.0000.0000.000
122C142GLY00.0050.00137.9090.0020.0020.0000.0000.0000.000
123C143PRO0-0.038-0.02338.5430.0020.0020.0000.0000.0000.000
124C144GLU-1-0.898-0.95236.8130.0570.0570.0000.0000.0000.000
125C145VAL0-0.021-0.00838.1340.0010.0010.0000.0000.0000.000
126C146VAL00.0190.01536.190-0.002-0.0020.0000.0000.0000.000
127C147LYS10.9840.98839.000-0.034-0.0340.0000.0000.0000.000
128C148THR00.011-0.01334.9970.0030.0030.0000.0000.0000.000
129C149GLY0-0.018-0.00534.643-0.003-0.0030.0000.0000.0000.000
130C150ALA0-0.045-0.00535.6000.0010.0010.0000.0000.0000.000
131C151SER0-0.002-0.02433.7950.0050.0050.0000.0000.0000.000
132C152VAL00.0170.01932.680-0.003-0.0030.0000.0000.0000.000
133C153LYS10.9410.97332.805-0.072-0.0720.0000.0000.0000.000
134C154ILE00.0080.02330.904-0.004-0.0040.0000.0000.0000.000
135C155SER00.0060.00332.8480.0040.0040.0000.0000.0000.000
136C156CYS0-0.0100.00627.8360.0050.0050.0000.0000.0000.000
137C157LYS10.9511.00433.971-0.069-0.0690.0000.0000.0000.000
138C158ALA0-0.005-0.00133.4560.0000.0000.0000.0000.0000.000
139C159SER0-0.059-0.03535.574-0.005-0.0050.0000.0000.0000.000
140C160GLY00.0880.03537.4330.0020.0020.0000.0000.0000.000
141C161TYR0-0.042-0.02431.2140.0040.0040.0000.0000.0000.000
142C162SER00.0150.01133.719-0.002-0.0020.0000.0000.0000.000
143C163PHE00.0780.02631.0860.0060.0060.0000.0000.0000.000
144C164THR00.006-0.01430.1230.0060.0060.0000.0000.0000.000
145C165GLY0-0.0070.00928.7320.0050.0050.0000.0000.0000.000
146C166TYR0-0.118-0.07526.7290.0040.0040.0000.0000.0000.000
147C167PHE0-0.018-0.00720.773-0.001-0.0010.0000.0000.0000.000
148C168ILE0-0.008-0.00724.948-0.008-0.0080.0000.0000.0000.000
149C169ASN00.017-0.02021.4120.0240.0240.0000.0000.0000.000
150C170TRP00.0470.02323.326-0.015-0.0150.0000.0000.0000.000
151C171VAL0-0.031-0.02023.0810.0100.0100.0000.0000.0000.000
152C172LYS10.9110.96824.244-0.101-0.1010.0000.0000.0000.000
153C173LYS10.8620.93125.495-0.088-0.0880.0000.0000.0000.000
154C174ASN00.0270.00227.980-0.002-0.0020.0000.0000.0000.000
155C175SER00.022-0.00229.8640.0030.0030.0000.0000.0000.000
156C176GLY0-0.015-0.01531.234-0.002-0.0020.0000.0000.0000.000
157C177LYS10.9801.00025.977-0.068-0.0680.0000.0000.0000.000
158C178SER00.0300.02722.447-0.002-0.0020.0000.0000.0000.000
159C179PRO0-0.040-0.01823.791-0.003-0.0030.0000.0000.0000.000
160C180GLU-1-0.857-0.91120.7540.1210.1210.0000.0000.0000.000
161C181TRP00.0030.00515.640-0.002-0.0020.0000.0000.0000.000
162C182ILE0-0.019-0.01218.8900.0100.0100.0000.0000.0000.000
163C183GLY00.0610.00918.8570.0160.0160.0000.0000.0000.000
164C184HIS0-0.076-0.00417.794-0.004-0.0040.0000.0000.0000.000
165C185ILE0-0.0090.00520.7800.0130.0130.0000.0000.0000.000
166C186SER00.0030.00722.095-0.010-0.0100.0000.0000.0000.000
167C187SER00.014-0.00623.794-0.004-0.0040.0000.0000.0000.000
168C188SER0-0.011-0.01327.161-0.004-0.0040.0000.0000.0000.000
169C189TYR00.0220.01823.942-0.007-0.0070.0000.0000.0000.000
170C190ALA0-0.0150.01124.9430.0040.0040.0000.0000.0000.000
171C191THR0-0.017-0.00119.1060.0050.0050.0000.0000.0000.000
172C192SER0-0.006-0.00820.865-0.003-0.0030.0000.0000.0000.000
173C193THR00.0090.01214.7570.0190.0190.0000.0000.0000.000
174C194TYR00.0190.01816.924-0.028-0.0280.0000.0000.0000.000
175C195ASN00.0280.01315.2040.0530.0530.0000.0000.0000.000
176C196GLN00.0500.02313.1280.0240.0240.0000.0000.0000.000
177C197LYS10.8560.91415.265-0.134-0.1340.0000.0000.0000.000
178C198PHE00.002-0.01118.026-0.023-0.0230.0000.0000.0000.000
179C199LYS10.9871.01616.399-0.269-0.2690.0000.0000.0000.000
180C200ASN0-0.020-0.01719.884-0.002-0.0020.0000.0000.0000.000
181C201LYS10.7570.88322.931-0.094-0.0940.0000.0000.0000.000
182C202ALA00.012-0.01123.487-0.010-0.0100.0000.0000.0000.000
183C203ALA00.0160.01823.9830.0100.0100.0000.0000.0000.000
184C204PHE0-0.033-0.02521.539-0.012-0.0120.0000.0000.0000.000
185C205THR0-0.011-0.00726.556-0.003-0.0030.0000.0000.0000.000
186C206VAL0-0.014-0.01328.3360.0010.0010.0000.0000.0000.000
187C207ASP-1-0.825-0.89830.8460.0740.0740.0000.0000.0000.000
188C208THR00.008-0.01232.8370.0010.0010.0000.0000.0000.000
189C209SER0-0.0060.00634.557-0.001-0.0010.0000.0000.0000.000
190C210SER0-0.036-0.02737.703-0.001-0.0010.0000.0000.0000.000
191C211SER0-0.027-0.00835.0960.0000.0000.0000.0000.0000.000
192C212THR00.0020.00034.6750.0010.0010.0000.0000.0000.000
193C213ALA0-0.0100.01129.3540.0030.0030.0000.0000.0000.000
194C214PHE0-0.015-0.03830.499-0.007-0.0070.0000.0000.0000.000
195C215MET00.0040.02126.8140.0120.0120.0000.0000.0000.000
196C216GLN0-0.051-0.02629.129-0.005-0.0050.0000.0000.0000.000
197C217LEU0-0.0040.00027.0680.0080.0080.0000.0000.0000.000
198C218ASN00.0550.02327.393-0.012-0.0120.0000.0000.0000.000
199C219SER00.0480.02029.2760.0010.0010.0000.0000.0000.000
200C220LEU0-0.064-0.01430.4250.0000.0000.0000.0000.0000.000
201C221THR00.0770.03329.668-0.007-0.0070.0000.0000.0000.000
202C222SER00.0590.00432.2650.0020.0020.0000.0000.0000.000
203C223GLU-1-0.945-0.95726.7430.0570.0570.0000.0000.0000.000
204C224ASP-1-0.812-0.89127.5940.0850.0850.0000.0000.0000.000
205C225SER00.0120.04229.5840.0020.0020.0000.0000.0000.000
206C226ALA0-0.054-0.02729.6100.0010.0010.0000.0000.0000.000
207C227VAL0-0.0200.00331.276-0.002-0.0020.0000.0000.0000.000
208C228TYR0-0.003-0.02626.7430.0090.0090.0000.0000.0000.000
209C229TYR0-0.0070.00028.268-0.006-0.0060.0000.0000.0000.000
210C231VAL00.014-0.02025.690-0.006-0.0060.0000.0000.0000.000
211C232ARG10.8850.96126.466-0.116-0.1160.0000.0000.0000.000
212C233SER00.0400.03122.4440.0020.0020.0000.0000.0000.000
213C234GLY00.0350.02524.781-0.007-0.0070.0000.0000.0000.000
214C235ASN00.0140.00823.0890.0210.0210.0000.0000.0000.000
215C236TYR00.0280.00623.095-0.004-0.0040.0000.0000.0000.000
216C237GLU-1-0.826-0.93423.6310.1950.1950.0000.0000.0000.000
217C238GLU-1-0.897-0.92425.9780.1330.1330.0000.0000.0000.000
218C239TYR0-0.037-0.01015.8090.0000.0000.0000.0000.0000.000
219C240ALA00.0130.01221.7980.0050.0050.0000.0000.0000.000
220C241MET0-0.030-0.01421.343-0.012-0.0120.0000.0000.0000.000
221C242ASP-1-0.744-0.84824.7940.1340.1340.0000.0000.0000.000
222C243TYR0-0.049-0.04428.447-0.007-0.0070.0000.0000.0000.000
223C244TRP00.002-0.00225.7250.0030.0030.0000.0000.0000.000
224C245GLY00.0480.03130.954-0.005-0.0050.0000.0000.0000.000
225C246GLN0-0.053-0.04233.3610.0020.0020.0000.0000.0000.000
226C247GLY0-0.0040.00633.130-0.002-0.0020.0000.0000.0000.000
227C248THR0-0.005-0.00833.326-0.002-0.0020.0000.0000.0000.000
228C249SER0-0.044-0.01633.6020.0030.0030.0000.0000.0000.000
229C250VAL00.0550.03232.833-0.002-0.0020.0000.0000.0000.000
230C251THR0-0.021-0.01634.4020.0000.0000.0000.0000.0000.000
231C252VAL0-0.017-0.00933.251-0.001-0.0010.0000.0000.0000.000
232C253SER0-0.026-0.01336.406-0.002-0.0020.0000.0000.0000.000